Tag: dna

Horizontal gene transfer

A mechanism for evolution where big chunks of DNA migrate between different species via bacteria. This results in faster and more sudden evolutionary branching than what you get with the more familiar mechanisms of sexual selection or random single-point

a massive network of recent gene exchange connecting bacteria from around the world: 10K unique genes flowing via HGT among 2235 bacterial genomes.

2008-10-05: The transfer can lead to recursive genomes

Scientists have discovered a copy of the entire genome of a bacterial parasite residing inside the genome of its host species. Lateral gene transfer may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, with dramatic implications for evolution. This may allow species to acquire new genes and functions extremely quickly.

2013-11-12: The transfer can also be time-shifted

You can compare it to a bunch of bacteria which poke around a trash pile looking for fragments they can use. Occasionally they hit some ‘second-hand gold,’ which they can use right away. At other times they run the risk of cutting themselves up. There is potential risk when multi-resistant bacteria exchange small fragments of ‘dangerous’ DNA, e.g., at hospitals, in biological waste and in wastewater.

2021-06-09: It might even happen in animals, perhaps via sperm.

The barriers to horizontal transfer in eukaryotes looked insurmountable until the herring genome was published. The herring genome holds many copies of transposons, mobile chunks of DNA that can copy and paste themselves in a genome, but they are absent from other fish with 1 exception. 3 of them flank the rainbow smelt’s AFP gene, in the same order seen around the herring AFP gene. These sequences are “definitive proof” that a small chunk of a herring chromosome made its way into a smelt’s. 94% of the transfers involved ray-finned fishes; less than 3% involved birds or mammals. The explanation could hinge on herring’s famously exuberant spawning efforts. The vast majority of sperm fail to find eggs, degrade, and release their DNA. The DNA could stick to the gametes from other species spawning in the same area, and then get dragged into an egg cell during fertilization.


2021-10-21: It also happens in the human microbiome, which is less surprising since that’s just bacteria.

when humans started to colonize the island of japan 40 ka ago, they did not have the genes for digesting seaweed. Bacteria in the japanese gut borrowed the necessary genes from marine bacteria via horizontal gene transfer, and since the adaption proved evolutionarily beneficial, it was preserved. of course, anti-GMO nuts fear this horizontal gene transfer the most (if they are scientifically literate enough to understand the concept, and not just spout confused concepts like “natural” vs “artificial”). it should be quite obvious from this awesome example that mammals have had to cope with horizontal gene transfer throughout their history. GMO offers nothing new we haven’t encountered before.

2022-10-28: Transfer via viruses or parasites could explain how HGT happens between Eukaryotes.

The involvement of viruses could also help to solve another puzzle about horizontal transfers in eukaryotes. For the transfers to occur, the traveling genes need to clear an entire series of hurdles. First they must get from the donor species to the new host species. Then they must get into the nucleus and ensconce themselves in the host genome. But getting into the genome of just any cell won’t do: In multicellular creatures like frogs and herrings, a gene won’t be passed down to the animal’s offspring unless it can sneak into a germline cell — a sperm or an egg.

Is there something about the environment of Madagascar that makes it a hot spot for gene transfers? The abundance of parasites on the island might also be a contributing factor. Leeches may bring blood containing the snake’s jumping gene into the frogs, or perhaps the jumping gene is already in the leech’s own genome from previous contacts with snakes. Then maybe an unidentified virus does the rest.

2023-01-19: Tycheposons

The findings describe a new class of genetic agents involved in horizontal gene transfer, in which genetic information is passed directly between organisms — whether of the same or different species — through means other than lineal descent. The researchers have dubbed the agents that carry out this transfer “tycheposons,” which are sequences of DNA that can include several entire genes as well as surrounding sequences, and can spontaneously separate out from the surrounding DNA. Then, they can be transported to other organisms by one or another possible carrier system including tiny bubbles known as vesicles that cells can produce from their own membranes.

2023-08-04: Mavericks, or Polintons, are large DNA transposons that contain genes with homology to viral proteins. They are the largest and most complex DNA transposons known. Mavericks are one of the long-sought vectors of horizontal gene transfer. They are related to giant viruses and virophages.

Mavericks are an ancient and fragmented class of jumping genes prevalent in the genomes of protists, fungi and animals, including humans. These massive mobile elements were initially assumed to be inactive, mutated relics of obsolete genes. But later research revealed that Mavericks can be reactivated, and that they can mediate horizontal gene transfer between some species of protists. Complete, intact Mavericks had never been characterized in a multicellular organism.

Before The Dawn

Using genetic anthropology to reconstruct the 90% of modern human history that is unrecorded. The discoveries are coming in fast; no doubt we’ll have a revival of alternative history books soon 🙂 We are beginning to uncover all the near-extinction events in our history that left marks in our mitochondria and Y-chromosomes. more vast and scary than any foundation myth.
2023-04-06: The 0-sum games that held humanity back for 300k years

The default condition of humans is no different from the default condition of other animals: Males fight each other over females. In humans, in apes, in deer, in insects. Despite apes being more intelligent than insects, they live in the same stability. And the same can be said about the human default: Despite being more intelligent than apes, humans are just as stuck in their ecological niches until the powerful among them get incentives to develop.

We are used to seeing human development as a line of progression. Step by step, generation after generation, humans are commonly thought to have added one small invention and observation after another, culminating in big breakthroughs and discoveries. I think it could be more useful to see human history as episodic. On some occasions, humans focused on the things that are possible to develop, that is, technology and teamwork. During most of the time, human males focused on a pursuit with little development potential: How to snatch as many females as possible from other males. However intelligent a species is, it will not develop as long as all its intelligence is used to play a 0-sum game.

DNA Nullomers

There must be some DNA or protein sequences that are not compatible with life, perhaps because they bind some essential cellular component, for example, and have therefore been selected out of circulation. There may also be some that are lethal in some species, but not others. We’re looking for those sequences.

looking for the shortest DNA strands not expressed anywhere: they might be too deadly. that reads almost like a script for a ‘dangers of GNR tech’ movie

Neanderthals

Pääbo may have the entire Neanderthal genome sequenced in the next 18 months.

2009-02-13: Draft Genome is announced. Bookmarked also for the nice facial reconstruction.

2009-05-17: We ate them

Neanderthals met a violent end at our hands and in some cases we ate them

2010-09-28: The cloning arguments are nothing new, but I was struck by

There were no cities when the Neanderthals went extinct, and at their population’s peak there may have only been 10k of them spread across Europe. A cloned Neanderthal might be missing the genetic adaptations we have evolved to cope with the world’s greater population density, whatever those adaptations might be. But, not everyone agrees that Neanderthals were so different from modern humans that they would automatically be shunned as outcasts.

2013-08-16: Neanderthal leather-working

Excavations of Neanderthal sites 40 ka BP have uncovered a kind of tool that leather workers still use to make hides more lustrous and water resistant. The bone tools, known as lissoirs, had previously been associated only with modern humans. The latest finds indicate that Neanderthals and modern humans might have invented the tools independently.

2016-05-25: 176 ka ago is unimaginably old. This is more than 15x older than Gobekli Tepe.

After drilling into the stalagmites and pulling out cylinders of rock, the team could see an obvious transition between 2 layers. On one side were old minerals that were part of the original stalagmites; on the other were newer layers that had been laid down after the fragments were broken off by the cave’s former users. By measuring uranium levels on either side of the divide, the team could accurately tell when each stalagmite had been snapped off for construction.

Their date? 176 ka ago, give or take a few millennia. “When I announced the age to Jacques, he asked me to repeat it because it was so incredible”. Outside Bruniquel Cave, the earliest, unambiguous human constructions are just 20 ka old. Most of these are ruins—collapsed collections of mammoth bones and deer antlers. By comparison, the Bruniquel stalagmite rings are well-preserved and far more ancient.

2016-05-27: More Neanderthal than human

In some spots of our genome, we are more Neanderthal than human. the sequences we inherited from archaic hominins helped us survive and reproduce

2017-01-15: Neanderthals Were People, Too

For millenniums, some scientists believe, before modern humans poured in from Africa, the climate in Europe was exceptionally unstable. The landscape kept flipping between temperate forest and cold, treeless steppe. The fauna that Neanderthals subsisted on kept migrating away, faster than they could. Though Neanderthals survived this turbulence, they were never able to build up their numbers. (Across all of Eurasia, at any point in history, “there probably weren’t enough of them to fill a stadium.”) With the demographics so skewed, even the slightest modern human advantage would be amplified tremendously: a single innovation, something like sewing needles, might protect just enough babies from the elements to lower the infant mortality rate and allow modern humans to conclusively overtake the Neanderthals. And yet Stringer is careful not to conflate innovation with superior intelligence. Innovation, too, can be a function of population size. “We live in an age where information, where good ideas, spread like wildfire, and we build on them. But it wasn’t like that 50 ka ago.” The more members your species has, the more likely 1 member will stumble on a useful new technology — and that, once stumbled upon, the innovation will spread; you need sufficient human tinder for those sparks of culture to catch.

2017-09-05: 200 ka Neanderthal Glue

As far back as 200 ka ago Neanderthals were using a tar-based adhesive to glue axe heads and spears to their handles. Researchers have attempted to recreate the Neander-glue, which could help scientists figure out just how technologically sophisticated the species was. Archaeologists have found lumps of adhesive tar likely made from birch bark at Neanderthal sites in Italy and Germany. But just how they made the substance puzzled researchers, especially because they did it without the aid of ceramic pots, which were used by later cultures to produce large quantities of tar.

2019-06-12: Did Neanderthals Speak?

Neanderthals had the anatomical properties to create the sounds that could form the basis of speech, though any words they produced would have sounded a bit unfamiliar to modern human ears

2020-03-04: long distance Neanderthals

Their intercontinental odyssey over 1000s of kilometers is a rarely observed case of long-distance dispersal in the Paleolithic and highlights the value of stone tools as culturally informative markers of ancient population movements.

2022-11-19: Interbreeding in Africa

The human-like Y chromosome entered the Neanderthal gene pool well before the migration out of Africa 80ka BP – perhaps 270ka BP. Which means that many of the Neanderthals that those migrants encountered must have already had human-like Y chromosomes! The Neanderthal Y chromosome and mitochondrial DNA are 2 new lines of evidence that point to a much more complex and ancient relationship between us and our closest cousins than we otherwise would have known.

2023-12-15: A new book, The Naked Neanderthal, looks interesting

Next, he explores evidence from skeletal remains for butchery and cannibalism of the dead in Neanderthal communities at Moula Guercy. Some researchers have proposed that such findings are a sign of starvation — evidence that Neanderthals were not able to adapt to the warm Eemian forests. Slimak concludes instead that these behaviors were a natural part of hominin social interactions, citing growing evidence from both archaeology and primatology that such practices were relatively common among humans right through prehistory.
Humans temporarily replaced local Neanderthals 54ka BP over an extraordinarily short time — potentially less than 1 year. The author uses this to argue that extermination, rather than assimilation, is the most likely explanation for the Neanderthals’ eventual extinction.